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Sample GSM11053 Query DataSets for GSM11053
Status Public on Dec 31, 2003
Title VREI_SJ064_2-19-01
Sample type RNA
 
Channel 1
Source name wt mixed reference RNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
Channel 2
Source name glp-4 adult prep 3 mRNA
Organism Caenorhabditis elegans
Extracted molecule total RNA
 
 
Description glp-4 adult prep 3 vs reference
 
Submission date Oct 09, 2003
Last update date May 28, 2005
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL446
Series (3)
GSE696 Gene expression in germ line
GSE715 glp-4 adults
GSE5069 Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans

Data table header descriptions
ID_REF
CH1_median Channel 1 (635 nm, Cy5, Reference) median pixel intensity
CH2_median Channel 2 (532 nm, Cy3, Experiment) median pixel intensity
CH1_back Channel 1 Background
CH2_back Channel 2 Background
CH1_MEAN Channel 1 Mean
CH2_MEAN
CH1_SD Channel 1 Standard Deviation
CH2_SD Channel 2 Standard Deviation
pixels Number of pixels used to determine signal.
bpixels Number of pixels used to determine background.
x X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
diameter diameter in µm of the feature-indicator
%>CH1_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 1
%>CH1_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 1
%>CH2_back+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, for Channel 2
%>CH2_back+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, for Channel 2
CH1_%Sat percentage of pixel saturation within feature for Channel 1
CH2_%Sat percentage of pixel saturation within feature for Channel 2
QUALITY
flag An extension of GenePix 3.0 flags described at http://twiki.med.yale.edu/twiki/bin/view/YMD/YMDFlagFields
ratio_calc (CH1_median-CH1_back)/(CH2_median-CH2_back)
VALUE log ratio (log2 of PRE_VALUE)
norm_factor Normalization factor calculated as described at http://twiki.med.yale.edu/twiki/bin/view/YMD/NormalizationAndFilterMethods
PRE_VALUE [(Experiment channel median intensity - background)/(Reference channel median intensity - background)]*(norm_factor)

Data table
ID_REF CH1_median CH2_median CH1_back CH2_back CH1_MEAN CH2_MEAN CH1_SD CH2_SD pixels bpixels x y diameter %>CH1_back+1SD %>CH1_back+2SD %>CH2_back+1SD %>CH2_back+2SD CH1_%Sat CH2_%Sat QUALITY flag ratio_calc VALUE norm_factor PRE_VALUE
2761835 6649 13814 331 225 11579 19751 10093 16667 120 524 1390 17820 120 92 90 95 93 0 0 1 0 2.151 1.9985573 1.858 3.996
2761837 6454 5897 309 204 5696 4952 3242 2744 120 489 1550 17810 120 92 89 94 90 0 0 1 0 .926 0.7832473 1.858 1.721
2761839 2214 1319 330 215 2225 1317 526 294 52 319 1720 17810 90 100 98 98 98 0 0 1 0 .586 0.1230043 1.858 1.089
2761841 11436 4205 342 207 10249 3650 6795 2242 80 411 1890 17810 110 100 95 96 93 0 0 1 0 .360 -0.5777673 1.858 .670
2761843 6489 32767 337 195 5281 30153 3879 24846 80 359 2030 17800 100 88 82 96 96 0 3 1 0 5.295 3.2980723 1.858 9.836
2761845 507 307 337 190 1355 1472 2106 2648 80 453 2190 17780 110 58 41 71 47 0 0 1 0 .688 0.3550163 1.858 1.279
2761847 11137 16933 344 198 9055 13516 5693 8410 120 523 2350 17790 120 96 94 100 100 0 0 1 0 1.551 1.5265703 1.858 2.881
2761849 2549 1602 362 197 2504 1441 896 523 80 333 2520 17800 100 96 95 100 97 0 0 1 0 .642 0.2558033 1.858 1.194
2761851 31437 1093 387 197 35606 1419 24060 993 156 627 2670 17800 140 99 99 89 88 6 0 1 0 .029 -4.2108973 1.858 .054
2761853 4815 2034 415 200 4481 1841 1357 663 80 386 2840 17800 110 100 96 98 96 0 0 1 0 .417 -0.3695953 1.858 .774
2761855 23079 32745 414 202 19516 28029 8365 9958 120 555 3000 17780 130 99 99 100 100 0 0 1 0 1.436 1.4152183 1.858 2.667
2761857 5143 1484 399 207 4492 1369 2214 711 120 459 3160 17800 120 100 99 96 92 0 0 1 0 .269 -1.0000003 1.858 .500
2761859 14373 4503 413 208 14889 4648 11287 3315 80 353 3320 17810 100 98 96 96 88 0 0 1 0 .308 -0.8059133 1.858 .572
2761861 2122 1123 416 199 2138 1146 443 228 52 324 3480 17800 90 100 98 100 100 0 0 1 0 .542 0.0086303 1.858 1.006
2761863 2594 2010 416 200 2247 1833 997 863 80 428 3640 17790 100 91 85 92 87 0 0 1 0 .831 0.6266733 1.858 1.544
2761865 3987 1908 417 195 3402 1698 1607 786 80 387 3810 17780 100 90 87 91 90 0 0 1 0 .480 -0.1665033 1.858 .891
2761867 16351 8548 402 193 13506 7615 8562 4479 80 353 3960 17770 100 98 97 100 100 0 0 1 0 .524 -0.0394883 1.858 .973
2761869 3136 1753 403 200 2807 1569 1127 686 80 386 4120 17780 100 96 90 90 83 0 0 1 0 .568 0.0786103 1.858 1.056
2761871 9203 5832 408 201 7778 4996 3529 2357 80 356 4280 17790 100 100 100 95 93 0 0 1 0 .640 0.2497493 1.858 1.189
2761873 9826 945 412 197 12667 1357 8463 952 156 642 4440 17760 140 98 96 96 93 0 0 1 0 .079 -2.7563313 1.858 .148

Total number of rows: 21632

Table truncated, full table size 2374 Kbytes.




Supplementary data files not provided
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